A Hidden Markov Model Approach for Identifying Differentially Methylated Sites and Regions for Beta-Valued DNA Methylation Data

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Documentation for package ‘betaHMM’ version 1.0.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

A	Accessors for the betaHMM package.
A-method	Accessors for the betaHMM package.
annotatedData	Accessors for the betaHMM package.
annotatedData-method	Accessors for the betaHMM package.
annotation_data	MethylationEPIC manifest data.
AUC	Accessors for the betaHMM package.
AUC-method	Accessors for the betaHMM package.
betaHMM	HMM for beta valued DNA data
betaHMM-method	HMM for beta valued DNA data
betaHMM-methods	HMM for beta valued DNA data
betaHMMResults	betaHMMResults object and constructor
betaHMMResults-class	betaHMMResults object and constructor
betaHMMrun	The betaHMM model parameter estimation function
chromosome_number	Accessors for the betaHMM package.
chromosome_number-method	Accessors for the betaHMM package.
dmcResults	dmcResults object and constructor
dmcResults-class	dmcResults object and constructor
dmc_identification	DMC identification from estimated betaHMM model parameters
dmc_identification-method	DMC identification from estimated betaHMM model parameters
dmc_identification-methods	DMC identification from estimated betaHMM model parameters
dmc_identification_run	DMC identification from estimated betaHMM model parameters
dmrResults	dmrResults object and constructor
dmrResults-class	dmrResults object and constructor
dmr_identification	DMR identification from DMCs identified
dmr_identification-method	DMR identification from DMCs identified
dmr_identification-methods	DMR identification from DMCs identified
dmr_identification_run	DMR identification from DMCs identified
hidden_states	Accessors for the betaHMM package.
hidden_states-method	Accessors for the betaHMM package.
K	Accessors for the betaHMM package.
K-method	Accessors for the betaHMM package.
llk	Accessors for the betaHMM package.
llk-method	Accessors for the betaHMM package.
model_parameters	Accessors for the betaHMM package.
model_parameters-method	Accessors for the betaHMM package.
N	Accessors for the betaHMM package.
N-method	Accessors for the betaHMM package.
pca_methylation_data	Simulated DNA methylation data
phi	Accessors for the betaHMM package.
phi-method	Accessors for the betaHMM package.
plot	Visualize results from 'betaHMM'/ 'dmc_identification'/ 'threshold_identification' functions.
plot-method	Visualize results from 'betaHMM'/ 'dmc_identification'/ 'threshold_identification' functions.
plot-methods	Visualize results from 'betaHMM'/ 'dmc_identification'/ 'threshold_identification' functions.
R	Accessors for the betaHMM package.
R-method	Accessors for the betaHMM package.
sample_annotation_file	MethylationEPIC manifest data.
sample_methylation_file	Simulated DNA methylation data
summary	Summarize results from the three betaHMM workflow functions
summary-method	Summarize results from the three betaHMM workflow functions
summary-methods	Summarize results from the three betaHMM workflow functions
tau	Accessors for the betaHMM package.
tau-method	Accessors for the betaHMM package.
threshold	Accessors for the betaHMM package.
threshold-method	Accessors for the betaHMM package.
threshold_identification	HMM for beta valued DNA data for a single treatment condition
threshold_identification-method	HMM for beta valued DNA data for a single treatment condition
threshold_identification-methods	HMM for beta valued DNA data for a single treatment condition
threshold_identification_run	Threshold indentification function
threshold_Results	threshold_Results object and constructor
threshold_Results-class	threshold_Results object and constructor
treatment_group	Accessors for the betaHMM package.
treatment_group-method	Accessors for the betaHMM package.
uncertainty	Accessors for the betaHMM package.
uncertainty-method	Accessors for the betaHMM package.